Multivariate Event Times (mets)

Implementation of various statistical models for multivariate event history data doi:10.1007/s10985-013-9244-x. Including multivariate cumulative incidence models doi:10.1002/sim.6016, and bivariate random effects probit models (Liability models) doi:10.1016/j.csda.2015.01.014. Modern methods for survival analysis, including regression modelling (Cox, Fine-Gray, Ghosh-Lin, Binomial regression) with fast computation of influence functions.

Installation

The development version may be installed directly from github (requires Rtools on windows and development tools (+Xcode) for Mac OS X):

remotes::install_github("kkholst/mets", dependencies="Suggests")

or to get development version

remotes::install_github("kkholst/mets",ref="develop")

Citation

To cite the mets package please use one of the following references

Thomas H. Scheike and Klaus K. Holst and Jacob B. Hjelmborg (2013). Estimating heritability for cause specific mortality based on twin studies. Lifetime Data Analysis. http://dx.doi.org/10.1007/s10985-013-9244-x

Klaus K. Holst and Thomas H. Scheike Jacob B. Hjelmborg (2015). The Liability Threshold Model for Censored Twin Data. Computational Statistics and Data Analysis. http://dx.doi.org/10.1016/j.csda.2015.01.014

BibTeX:

@Article{,
  title={Estimating heritability for cause specific mortality based on twin studies},
  author={Scheike, Thomas H. and Holst, Klaus K. and Hjelmborg, Jacob B.},
  year={2013},
  issn={1380-7870},
  journal={Lifetime Data Analysis},
  doi={10.1007/s10985-013-9244-x},
  url={http://dx.doi.org/10.1007/s10985-013-9244-x},
  publisher={Springer US},
  keywords={Cause specific hazards; Competing risks; Delayed entry;
        Left truncation; Heritability; Survival analysis},
  pages={1-24},
  language={English}
}

@Article{,
  title={The Liability Threshold Model for Censored Twin Data},
  author={Holst, Klaus K. and Scheike, Thomas H. and Hjelmborg, Jacob B.},
  year={2015},
  doi={10.1016/j.csda.2015.01.014},
  url={http://dx.doi.org/10.1016/j.csda.2015.01.014},
  journal={Computational Statistics and Data Analysis}
}

Examples 

library("mets")

data(prt) ## Prostate data example (sim)

## Bivariate competing risk, concordance estimates
p33 <- bicomprisk(Event(time,status)~strata(zyg)+id(id),
                  data=prt, cause=c(2,2), return.data=1, prodlim=TRUE)
#> Strata 'DZ'
#> Strata 'MZ'

p33dz <- p33$model$"DZ"$comp.risk
p33mz <- p33$model$"MZ"$comp.risk

## Probability weights based on Aalen's additive model (same censoring within pair)
prtw <- ipw(Surv(time,status==0)~country+zyg, data=prt,
            obs.only=TRUE, same.cens=TRUE, 
            cluster="id", weight.name="w")

## Marginal model (wrongly ignoring censorings)
bpmz <- biprobit(cancer~1 + cluster(id), 
                 data=subset(prt,zyg=="MZ"), eqmarg=TRUE)

## Extended liability model
bpmzIPW <- biprobit(cancer~1 + cluster(id),
                    data=subset(prtw,zyg=="MZ"),
                    weights="w")
smz <- summary(bpmzIPW)

## Concordance
plot(p33mz,ylim=c(0,0.1),axes=FALSE, automar=FALSE,atrisk=FALSE,background=TRUE,background.fg="white")
axis(2); axis(1)

abline(h=smz$prob["Concordance",],lwd=c(2,1,1),col="darkblue")
## Wrong estimates:
abline(h=summary(bpmz)$prob["Concordance",],lwd=c(2,1,1),col="lightgray", lty=2)

plot of chunk ex1